ASTRAL-Pro 2: ultrafast species tree reconstruction from multi-copy gene family trees.

Abstract

Species tree inference from multi-copy gene trees has long been a challenge in phylogenomics. The recent method ASTRAL-Pro has made strides by enabling multi-copy gene family trees as input and has been quickly adopted. Yet, its scalability, especially memory usage, needs to improve to accommodate the ever-growing dataset size. We present ASTRAL-Pro 2, an ultrafast and memory efficient version of ASTRAL-Pro that adopts a placement-based optimization algorithm for significantly better scalability without sacrificing accuracy. The source code and binary files are publicly available at https://github.com/chaoszhang/ASTER; data are available at https://github.com/chaoszhang/A-Pro2_data. Supplementary data are available at Bioinformatics online.